There are three duplexes built on one site, correct? Need clarification when you say the improvements are on separate lot numbers, but one parcel number. If each duplex is on a separate site, then I assume your used that site area for each duplex. Perhaps upload the plat, to clarify.
You have one parcel made up of multiple lots which is common in many places. You should not have appraised just two of the duplexes in my opinion. I think you have a problem and if they have actually sent a complaint to the state you need to call E and O tomorrow.